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- PDB-2xt2: Structure of the pentapeptide repeat protein AlbG, a resistance f... -

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Basic information

Entry
Database: PDB / ID: 2xt2
TitleStructure of the pentapeptide repeat protein AlbG, a resistance factor for the topoisomerase poison albicidin.
ComponentsMCBG-LIKE PROTEIN
KeywordsCELL CYCLE / RIGHT HANDED QUADRILATERAL BETA HELIX
Function / homologyE3 ubiquitin-protein ligase SopA / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Pectate Lyase C-like / acyltransferase activity / 3 Solenoid / Mainly Beta / McbG-like protein
Function and homology information
Biological speciesXANTHOMONAS ALBILINEANS (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.999 Å
AuthorsVetting, M.W. / Hegde, S.S. / Blanchard, J.S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Pentapeptide-Repeat Proteins that Act as Topoisomerase Poison Resistance Factors Have a Common Dimer Interface.
Authors: Vetting, M.W. / Hegde, S.S. / Zhang, Y. / Blanchard, J.S.
History
DepositionOct 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MCBG-LIKE PROTEIN
B: MCBG-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9296
Polymers45,5452
Non-polymers3844
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-52.7 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.710, 90.242, 55.983
Angle α, β, γ (deg.)90.00, 100.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MCBG-LIKE PROTEIN / ALBG


Mass: 22772.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XANTHOMONAS ALBILINEANS (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q70C34
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 51.4 % / Description: NONE
Crystal growpH: 6.3
Details: COMBINING NATIVE PROTEIN, 2 UL OF 20 MG ML-1, 20 MM TRIS PH 8.0, 1 MM DTT WITH PRECIPITANT, 2 UL OF 1 M MGSO4, 100 MM LISO4, 100 MM ADA PH 6.3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU-MSC RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GRAPHIC CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 29136 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 24.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 8.7 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.999→22.56 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 1456 5.1 %
Rwork0.1634 --
obs0.1661 28848 98.44 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.99 Å2 / ksol: 0.425 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3954 Å20 Å27.0819 Å2
2---4.6858 Å20 Å2
3---7.0811 Å2
Refinement stepCycle: LAST / Resolution: 1.999→22.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 20 198 3333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013203
X-RAY DIFFRACTIONf_angle_d1.2044321
X-RAY DIFFRACTIONf_dihedral_angle_d12.9061159
X-RAY DIFFRACTIONf_chiral_restr0.087469
X-RAY DIFFRACTIONf_plane_restr0.005564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.07040.25011400.19232625X-RAY DIFFRACTION95
2.0704-2.15330.24091310.16332721X-RAY DIFFRACTION98
2.1533-2.25120.24931410.14732755X-RAY DIFFRACTION99
2.2512-2.36980.20781390.15422728X-RAY DIFFRACTION99
2.3698-2.51810.22771360.16152777X-RAY DIFFRACTION99
2.5181-2.71220.26161500.18442734X-RAY DIFFRACTION99
2.7122-2.98460.25491500.1832777X-RAY DIFFRACTION100
2.9846-3.41520.21091730.17442759X-RAY DIFFRACTION100
3.4152-4.29790.17521360.13432789X-RAY DIFFRACTION99
4.2979-22.56190.19461600.16962727X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16320.1501-0.06290.30480.10930.2276-0.0597-0.1242-0.265-0.1953-0.0498-0.08920.31050.0284-00.24120.06810.06320.17910.06560.282219.06339.802218.5964
20.10230.03670.06010.1156-0.03910.09790.0048-0.17380.0925-0.1532-0.0634-0.0874-0.05350.2148-0.00010.1730.03430.03810.16950.03470.185319.743949.780119.4354
30.02310.15860.08280.72340.03260.2008-0.031-0.0007-0.0138-0.0607-0.1171-0.39980.08250.1145-00.14360.01440.00350.15880.02460.201422.953561.015318.662
40.02980.1296-0.03940.1453-0.05040.00550.0472-0.21940.2754-0.0523-0.0777-0.4494-0.15830.1527-0.00020.1936-0.04740.0350.1660.02080.325625.982775.129516.1988
5-0.0041-0.0049-0.00720.01480.01350.0017-0.2796-0.13490.02840.0865-0.15260.2391-0.0308-0.1786-00.2348-0.0807-0.04340.25830.00730.390123.621187.83349.1109
60.0123-0.00940.0034-0.0332-0.02330.00390.11570.00690.2312-0.0262-0.1118-0.0929-0.19070.1887-0.00870.1884-0.0256-0.03620.1114-0.04080.145148.5483125.619210.2434
70.27030.43930.04030.38720.04820.13510.0712-0.10260.06390.0102-0.07170.0237-0.1368-0.0498-0.02810.1440.0274-0.00620.1547-0.0250.071642.9459118.801112.4923
80.51880.2766-0.47370.5202-0.20130.14660.0432-0.2313-0.1062-0.1101-0.04030.0349-0.04690.03840.0250.0603-0.0062-0.03510.15240.05190.033936.177103.228614.6499
9-0.00510.0125-0.01620.06290.08870.0553-0.2557-0.3891-0.3747-0.31390.1950.25470.3021-0.2205-00.1568-0.00880.01190.27870.14240.315927.591191.341617.7108
100.00660.0753-0.02620.06730.01540.0149-0.1434-0.2587-0.2344-0.114-0.0039-0.5037-0.1541-0.4204-0.00050.2324-0.07040.02190.16820.0960.424232.983381.70114.9353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 9:67)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 68:89)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 90:167)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 168:193)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 194:199)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 1:26)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 27:75)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 76:167)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 168:181)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 182:199)

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